Dear All, I am facing some problems with RGUI loading dba.count with my dataset, > setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data/ChIP- seq Roberto/Analisi_PK/DiffBind/H3K27me3/") > library("DiffBind") > test= dba(sampleSheet='database.csv') ES_H3K27 ES H3K27 1 1 raw CMN_H3K27 CMN H3K27 1 1 raw CMA_H3K27 CMA H3K27 1 1 raw > test=dba.count(test) AppName: rgui.exe AppVer: 2.150.58871.0 ModName: diffbind.dll ModVer: 0.0.0.0 Offset: 00003be1 Did anyone faced the same problem? which are the memory requirements to run DiffBind? Thanks, Paolo

Hi, Paolo, DiffBind uses quite a lot of memory for the dba.count step, because it loads the whole data file into memory. (In hindsight, not the best design choice...) Try running with parallelization turned off: > test=dba.count(test,bParallel=F) so that it only loads one file at a time, to reduce the memory footprint. For the upcoming release, we'll probably fix this, at the cost of somewhat slower counting. How much RAM does your machine have? Cheers, - Gord On 2012/07/30 11:00, "Paolo Kunderfranco" <paolo.kunderfranco at="" gmail.com=""> wrote: > Dear All, > I am facing some problems with RGUI loading dba.count with my dataset, > >> setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data/ChIP- seq >> Roberto/Analisi_PK/DiffBind/H3K27me3/") > >> library("DiffBind") > >> test= dba(sampleSheet='database.csv') > ES_H3K27 ES H3K27 1 1 raw > CMN_H3K27 CMN H3K27 1 1 raw > CMA_H3K27 CMA H3K27 1 1 raw > >> test=dba.count(test) > AppName: rgui.exe AppVer: 2.150.58871.0 ModName: diffbind.dll > ModVer: 0.0.0.0 Offset: 00003be1 > > Did anyone faced the same problem? which are the memory requirements > to run DiffBind? > Thanks, > Paolo > > NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}